Merge pull request #70 from GEOS-ESM/develop

GitFlow: merge develop into main for release

MIT_GEOS5PlugMod/configs/c90_llc90_03/code/CPP_EEOPTIONS.h

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+#ifndef _CPP_EEOPTIONS_H_
+#define _CPP_EEOPTIONS_H_
+
+CBOP
+C     !ROUTINE: CPP_EEOPTIONS.h
+C     !INTERFACE:
+C     include "CPP_EEOPTIONS.h"
+C
+C     !DESCRIPTION:
+C     *==========================================================*
+C     | CPP\_EEOPTIONS.h                                         |
+C     *==========================================================*
+C     | C preprocessor "execution environment" supporting        |
+C     | flags. Use this file to set flags controlling the        |
+C     | execution environment in which a model runs - as opposed |
+C     | to the dynamical problem the model solves.               |
+C     | Note: Many options are implemented with both compile time|
+C     |       and run-time switches. This allows options to be   |
+C     |       removed altogether, made optional at run-time or   |
+C     |       to be permanently enabled. This convention helps   |
+C     |       with the data-dependence analysis performed by the |
+C     |       adjoint model compiler. This data dependency       |
+C     |       analysis can be upset by runtime switches that it  |
+C     |       is unable to recoginise as being fixed for the     |
+C     |       duration of an integration.                        |
+C     |       A reasonable way to use these flags is to          |
+C     |       set all options as selectable at runtime but then  |
+C     |       once an experimental configuration has been        |
+C     |       identified, rebuild the code with the appropriate  |
+C     |       options set at compile time.                       |
+C     *==========================================================*
+CEOP
+
+C     In general the following convention applies:
+C     ALLOW  - indicates an feature will be included but it may
+C     CAN      have a run-time flag to allow it to be switched
+C              on and off.
+C              If ALLOW or CAN directives are "undef'd" this generally
+C              means that the feature will not be available i.e. it
+C              will not be included in the compiled code and so no
+C              run-time option to use the feature will be available.
+C
+C     ALWAYS - indicates the choice will be fixed at compile time
+C              so no run-time option will be present
+
+C=== Macro related options ===
+C--   Control storage of floating point operands
+C     On many systems it improves performance only to use
+C     8-byte precision for time stepped variables.
+C     Constant in time terms ( geometric factors etc.. )
+C     can use 4-byte precision, reducing memory utilisation and
+C     boosting performance because of a smaller working set size.
+C     However, on vector CRAY systems this degrades performance.
+C     Enable to switch REAL4_IS_SLOW from genmake2 (with LET_RS_BE_REAL4):
+#ifdef LET_RS_BE_REAL4
+#undef REAL4_IS_SLOW
+#else /* LET_RS_BE_REAL4 */
+#define REAL4_IS_SLOW
+#endif /* LET_RS_BE_REAL4 */
+
+C--   Control use of "double" precision constants.
+C     Use D0 where it means REAL*8 but not where it means REAL*16
+#define D0 d0
+
+C=== IO related options ===
+C--   Flag used to indicate whether Fortran formatted write
+C     and read are threadsafe. On SGI the routines can be thread
+C     safe, on Sun it is not possible - if you are unsure then
+C     undef this option.
+#undef FMTFTN_IO_THREAD_SAFE
+
+C--   Flag used to indicate whether Binary write to Local file (i.e.,
+C     a different file for each tile) and read are thread-safe.
+#undef LOCBIN_IO_THREAD_SAFE
+
+C--   Flag to turn off the writing of error message to ioUnit zero
+#undef DISABLE_WRITE_TO_UNIT_ZERO
+
+C--   Alternative formulation of BYTESWAP, faster than
+C     compiler flag -byteswapio on the Altix.
+#undef FAST_BYTESWAP
+
+C--   Flag to turn on old default of opening scratch files with the
+C     STATUS='SCRATCH' option. This method, while perfectly FORTRAN-standard,
+C     caused filename conflicts on some multi-node/multi-processor platforms
+C     in the past and has been replace by something (hopefully) more robust.
+#undef USE_FORTRAN_SCRATCH_FILES
+
+C--   Flag defined for eeboot_minimal.F, eeset_parms.F and open_copy_data_file.F
+C     to write STDOUT, STDERR and scratch files from process 0 only.
+C WARNING: to use only when absolutely confident that the setup is working
+C     since any message (error/warning/print) from any proc <> 0 will be lost.
+#undef SINGLE_DISK_IO
+
+C=== MPI, EXCH and GLOBAL_SUM related options ===
+C--   Flag turns off MPI_SEND ready_to_receive polling in the
+C     gather_* subroutines to speed up integrations.
+#undef DISABLE_MPI_READY_TO_RECEIVE
+
+C--   Control MPI based parallel processing
+CXXX We no longer select the use of MPI via this file (CPP_EEOPTIONS.h)
+CXXX To use MPI, use an appropriate genmake2 options file or use
+CXXX genmake2 -mpi .
+CXXX #undef  ALLOW_USE_MPI
+
+C--   Control use of communication that might overlap computation.
+C     Under MPI selects/deselects "non-blocking" sends and receives.
+#undef  ALLOW_ASYNC_COMMUNICATION
+#undef  ALWAYS_USE_ASYNC_COMMUNICATION
+C--   Control use of communication that is atomic to computation.
+C     Under MPI selects/deselects "blocking" sends and receives.
+#define ALLOW_SYNC_COMMUNICATION
+#undef  ALWAYS_USE_SYNC_COMMUNICATION
+
+C--   Control XY periodicity in processor to grid mappings
+C     Note: Model code does not need to know whether a domain is
+C           periodic because it has overlap regions for every box.
+C           Model assume that these values have been
+C           filled in some way.
+#undef  ALWAYS_PREVENT_X_PERIODICITY
+#undef  ALWAYS_PREVENT_Y_PERIODICITY
+#define CAN_PREVENT_X_PERIODICITY
+#define CAN_PREVENT_Y_PERIODICITY
+
+C--   disconnect tiles (no exchange between tiles, just fill-in edges
+C     assuming locally periodic subdomain)
+#undef DISCONNECTED_TILES
+
+C--   Always cumulate tile local-sum in the same order by applying MPI allreduce
+C     to array of tiles ; can get slower with large number of tiles (big set-up)
+#define GLOBAL_SUM_ORDER_TILES
+
+C--   Alternative way of doing global sum without MPI allreduce call
+C     but instead, explicit MPI send & recv calls. Expected to be slower.
+#undef GLOBAL_SUM_SEND_RECV
+
+C--   Alternative way of doing global sum on a single CPU
+C     to eliminate tiling-dependent roundoff errors. Note: This is slow.
+#undef  CG2D_SINGLECPU_SUM
+
+C=== Other options (to add/remove pieces of code) ===
+C--   Flag to turn on checking for errors from all threads and procs
+C     (calling S/R STOP_IF_ERROR) before stopping.
+#define USE_ERROR_STOP
+
+C--   Control use of communication with other component:
+C     allow to import and export from/to Coupler interface.
+#undef COMPONENT_MODULE
+
+C--   Activate some pieces of code for coupling to GEOS AGCM
+#define HACK_FOR_GMAO_CPL
+
+C=== And define Macros ===
+#include "CPP_EEMACROS.h"
+
+#endif /* _CPP_EEOPTIONS_H_ */

MIT_GEOS5PlugMod/configs/c90_llc90_03/code/CPP_OPTIONS.h

@@ -0,0 +1,149 @@
+#ifndef CPP_OPTIONS_H
+#define CPP_OPTIONS_H
+
+CBOP
+C !ROUTINE: CPP_OPTIONS.h
+C !INTERFACE:
+C #include "CPP_OPTIONS.h"
+
+C !DESCRIPTION:
+C *==================================================================*
+C | main CPP options file for the model:
+C | Control which optional features to compile in model/src code.
+C *==================================================================*
+CEOP
+
+C CPP flags controlling particular source code features
+
+C o Turn off capping of precip with snowprecip. This will elimnates one
+C   forward loop in the adjoint code.
+#define Turnoff_capping_precip_by_snowprecip 
+
+C o Use 3d shiTransCoeffT and shiTransCoeffS
+#define ALLOW_shiTransCoeff_3d
+
+C o Shortwave heating as extra term in external_forcing.F
+C Note: this should be a run-time option
+#define SHORTWAVE_HEATING
+
+C o Include/exclude Geothermal Heat Flux at the bottom of the ocean
+#define ALLOW_GEOTHERMAL_FLUX
+
+C o Include/exclude phi_hyd calculation code
+#define INCLUDE_PHIHYD_CALCULATION_CODE
+
+C o Include/exclude call to S/R CONVECT
+#define INCLUDE_CONVECT_CALL
+
+
+C o Include/exclude call to S/R CALC_DIFFUSIVITY
+#define INCLUDE_CALC_DIFFUSIVITY_CALL
+
+C o Allow full 3D specification of vertical diffusivity
+#define ALLOW_3D_DIFFKR
+
+C o Allow latitudinally varying BryanLewis79 vertical diffusivity
+#undef ALLOW_BL79_LAT_VARY
+
+C o Include/exclude Implicit vertical advection code
+#define INCLUDE_IMPLVERTADV_CODE
+
+C o Include/exclude AdamsBashforth-3rd-Order code
+#undef ALLOW_ADAMSBASHFORTH_3
+
+C o Include/exclude nonHydrostatic code
+#undef ALLOW_NONHYDROSTATIC
+#undef ALLOW_QHYD_STAGGER_TS
+
+C o Allow to account for heating due to friction (and momentum dissipation)
+#undef ALLOW_FRICTION_HEATING
+
+C o Allow mass source or sink of Fluid in the interior
+C   (3-D generalisation of oceanic real-fresh water flux)
+#define ALLOW_ADDFLUID
+
+C o Include pressure loading code
+#define ATMOSPHERIC_LOADING
+#ifdef ATMOSPHERIC_LOADING
+#define ALLOW_IB_CORR 
+#endif
+
+C o Calculate Phi-Hydrostatic at r-lower boundary during initialization.
+C   Needed for obp cost. Otherwise, the first record of m_bp is wrong,
+C   because phiHydLow is zero.
+#define CALC_PHI_RLOW_INI
+
+C o exclude/allow external forcing-fields load
+C   this allows to read & do simple linear time interpolation of oceanic
+C   forcing fields, if no specific pkg (e.g., EXF) is used to compute them.
+#undef EXCLUDE_FFIELDS_LOAD
+
+C o Include/exclude balancing surface forcing fluxes code
+#undef ALLOW_BALANCE_FLUXES
+
+C o Include/exclude balancing surface forcing relaxation code
+#undef ALLOW_BALANCE_RELAX
+
+C o Include/exclude GM-like eddy stress in momentum code
+#undef ALLOW_EDDYPSI
+
+C o Use "Exact Convervation" of fluid in Free-Surface formulation
+C   so that d/dt(eta) is exactly equal to - Div.Transport
+#define EXACT_CONSERV
+
+C o Allow the use of Non-Linear Free-Surface formulation
+C   this implies that surface thickness (hFactors) vary with time
+#define NONLIN_FRSURF
+# undef DISABLE_RSTAR_CODE
+#undef DISABLE_SIGMA_CODE
+
+C o Include/exclude code for single reduction Conjugate-Gradient solver
+#undef ALLOW_SRCG
+
+C o Choices for implicit solver routines solve_*diagonal.F
+C   The following has low memory footprint, but not suitable for AD
+#undef SOLVE_DIAGONAL_LOWMEMORY
+C   The following one suitable for AD but does not vectorize
+#define SOLVE_DIAGONAL_KINNER
+
+C o ALLOW isotropic scaling of harmonic and bi-harmonic terms when
+C   using an locally isotropic spherical grid with (dlambda) x (dphi*cos(phi))
+C *only for use on a lat-lon grid*
+C   Setting this flag here affects both momentum and tracer equation unless
+C   it is set/unset again in other header fields (e.g., GAD_OPTIONS.h).
+C   The definition of the flag is commented to avoid interference with
+C   such other header files.
+C   The preferred method is specifying a value for viscAhGrid or viscA4Grid
+C   in data which is then automatically scaled by the grid size;
+C   the old method of specifying viscAh/viscA4 and this flag is provided
+C   for completeness only (and for use with the adjoint).
+C#define ISOTROPIC_COS_SCALING
+
+C o This flag selects the form of COSINE(lat) scaling of bi-harmonic term.
+C *only for use on a lat-lon grid*
+C   Has no effect if ISOTROPIC_COS_SCALING is undefined.
+C   Has no effect on vector invariant momentum equations.
+C   Setting this flag here affects both momentum and tracer equation unless
+C   it is set/unset again in other header fields (e.g., GAD_OPTIONS.h).
+C   The definition of the flag is commented to avoid interference with
+C   such other header files.
+C#define COSINEMETH_III
+
+C o Use "OLD" UV discretisation near boundaries (*not* recommended)
+C   Note - only works with pkg/mom_fluxform and "no_slip_sides=.FALSE."
+C          because the old code did not have no-slip BCs
+#undef OLD_ADV_BCS
+
+C o Use LONG.bin, LATG.bin, etc., initialization for ini_curviliear_grid.F
+C   Default is to use "new" grid files (OLD_GRID_IO undef) but OLD_GRID_IO
+C   is still useful with, e.g., single-domain curvilinear configurations.
+#undef OLD_GRID_IO
+
+C o Use old EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility)
+#undef USE_OLD_EXTERNAL_FORCING
+
+C o Execution environment support options
+#include "CPP_EEOPTIONS.h"
+
+#endif /* CPP_OPTIONS_H */
+

MIT_GEOS5PlugMod/configs/c90_llc90_03/code/DIAGNOSTICS_SIZE.h

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+C $Header: /u/gcmpack/MITgcm_contrib/ecco_utils/ecco_v4_release3_devel/code/DIAGNOSTICS_SIZE.h,v 1.1 2017/05/04 17:46:37 ou.wang Exp $
+C $Name:  $
+
+
+C     Diagnostics Array Dimension
+C     ---------------------------
+C     ndiagMax   :: maximum total number of available diagnostics
+C     numlists   :: maximum number of diagnostics list (in data.diagnostics)
+C     numperlist :: maximum number of active diagnostics per list (data.diagnostics)
+C     numLevels  :: maximum number of levels to write    (data.diagnostics)
+C     numDiags   :: maximum size of the storage array for active 2D/3D diagnostics
+C     nRegions   :: maximum number of regions (statistics-diagnostics)
+C     sizRegMsk  :: maximum size of the regional-mask (statistics-diagnostics)
+C     nStats     :: maximum number of statistics (e.g.: aver,min,max ...)
+C     diagSt_size:: maximum size of the storage array for statistics-diagnostics
+C Note : may need to increase "numDiags" when using several 2D/3D diagnostics,
+C  and "diagSt_size" (statistics-diags) since values here are deliberately small.
+      INTEGER    ndiagMax
+      INTEGER    numlists, numperlist, numLevels
+      INTEGER    numDiags
+      INTEGER    nRegions, sizRegMsk, nStats
+      INTEGER    diagSt_size
+      PARAMETER( ndiagMax = 700 )
+      PARAMETER( numlists = 300, numperlist = 30, numLevels=5*Nr )
+      PARAMETER( numDiags = 4000 )
+      PARAMETER( nRegions = 20 , sizRegMsk = 1 , nStats = 4 )
+      PARAMETER( diagSt_size = 50*Nr )
+
+
+CEH3 ;;; Local Variables: ***
+CEH3 ;;; mode:fortran ***
+CEH3 ;;; End: ***

MIT_GEOS5PlugMod/configs/c90_llc90_03/code/GGL90_OPTIONS.h

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+C     *=============================================================*
+C     | GGL90_OPTIONS.h
+C     | o CPP options file for GGL90 package.
+C     *=============================================================*
+C     | Use this file for selecting options within the GGL90
+C     | package.
+C     *=============================================================*
+
+#ifndef GGL90_OPTIONS_H
+#define GGL90_OPTIONS_H
+#include "PACKAGES_CONFIG.h"
+#include "CPP_OPTIONS.h"
+
+#ifdef ALLOW_GGL90
+C     Package-specific Options & Macros go here
+
+C     Enable horizontal diffusion of TKE.
+#undef ALLOW_GGL90_HORIZDIFF
+
+C     Use horizontal averaging for viscosity and diffusivity as
+C     originally implemented in OPA.
+#define ALLOW_GGL90_SMOOTH
+
+C     allow IDEMIX model
+#undef ALLOW_GGL90_IDEMIX
+
+C     include Langmuir circulation parameterization
+#undef ALLOW_GGL90_LANGMUIR
+
+#endif /* ALLOW_GGL90 */
+#endif /* GGL90_OPTIONS_H */